Transcription Networks: a global view
26-28 May 2005
Madrid, Spain

Organisers:

Ildefonso Cases, CNB-CSIC, Madrid, Spain
Alfonso Valencia, CNB-CSIC, Madrid, Spain

Draft Report

Summary

The "ESF workshop on Transcription Networks: a Global View" was held in Madrid 26-28 May, in the "Residencia de Estudiantes". This event put together 14 speakers from 7 countries and 64 participants from 10 countries. These numbers, which were above our initial estimations, are indicative of the relevance of the selected topic and the quality of the programme.

The workshop was divided into three main sessions: "Modeling networks", "Evolution of transcription networks" and "Interaction with other biological processes"; each of them including between 2 and 6 main speakers and 2 short presentations selected from the posters, and a 2 hours poster session with 23 posters.

The focused topic of the meeting together with its size, allowed for ample discussion in a lively atmosphere, which result in a scientifically fruitful meeting. The impact and quality of the workshop made it worthy of a report in the "Genome Biology" Journal. [Teichmann, Bornberg-Bauer & Luscombe. "Transcriptional networking." Genome Biology 2005;6(9):344]

Scientific Content

The meeting was organized in three lecture sessions and one poster session. First session included talks by Ricard Solé (UPF, Barcelona, Spain), who showed theoretical works on the mechanisms that could be behind the evolution and properties of regulatory networks, and in a more general case, biological networks. These models are bases in biological relevant proceses as duplication, deletion and mutation. The second lecture was by Hidde de Jong (INRIA, Montbonnot, France) who explained several mathematical tools for the modeling of bacterial transcription networks. The last two talks of the session were by Alvis Brazma (EBI, Cambridge, UK) and Roderic Guigó (UPF, Barcelona, Spain). Dr. Brazma explained how transcription networks can be studied at different levels of detail, from whole genomes to particular systems, and how to use control-logistics models to model them. Dr. Guigo showed the recent development in the annotation of the human genome, and the mapping of transcription relevant signals in the upstream regions of human genes. Two short presentations selected from posters were also included in this session, one by J. T. Kim (University of East Anglia, Norwich, UK) who presented a framework for modeling gene expression dynamics and a network reconstruction and the other by A. Garcia-Lomana (IMIM, Barcelona, Spain) who presented a software package for simulation of regulatory networks.

The second session, the largest of the workshop was devoted to evolution of transcription networks. Julio Collado Vides (UNAM, Cuernavaca, Mexico) and Sarah Teichmann (MRC-LMB, Cambridge, UK) discussed different approaches to describe and study Transcription Factors in prokaryotes (Dr. Collado) and eukaryotes (Dr. Teichamn). One the other hand, Dr. Mar Albá (UPF, Barcelona, Spain) discussed different methods to detect the other main component of transcription networks: promoters and transcription factor binding sites, in this case in the mouse genome, and by comparison with other metazoan genomes, suggested several models of evolution. A new algorithm for the detection of transcription factor binding sites was presented by R. Janky (ULB, Brussels, Belgium), in one of the selected short talks. How these elements are arranged in chromosomes and the relevance of the structure of the genomes was the topic of Dr. Francois Kepes (Genopole, Evry, France). This subject was also discussed by Dr. Ussery (CBS, Lyngby, Denmark), but in the context of bacterial chromosomes, in one of the selected short talks. Dr. Eric Bornberg-Bauer (University of Muenster, Germany) discussed about transcription factors interaction, in particular dimerization. This property of many transcription factors is essential for the dynamical properties of the regulatory networks. Relevant sequence motifs important for this interaction were also the subject of a short talk by Dr. Hancock (MRC-MGU, Harwell , UK) . Dr. Martjin Huynen detailed in his talk a model for the evolution of large molecular complexes, and the role of duplication and the establishment of new interactions in the formation of complex networks, while Dr. Frank Holstege (University Medical Center, Utrech, The Netherlands) presented how the combination of expression data and deletion experiments could be used for the elucidation of transcription networks. This session was completed with a short talk by Dr. Luscombe (EBI, Cambridge, UK) showing the different properties of the active regulatory networks under different physiological conditions.

The last session of the workshop included talks by Dr. Jacques van Helden (ULB, Brussels, Belgium) who discussed the relation between metabolic pathways and regulatory networks and how transcription information can help in the modeling of metabolic pathways, Dr. Joaquin Dopazo (CIPF, Valencia, Spain) who showed powerful techniques for the inference of transcription networks from DNA microarray expression data, and Dr. Benno Schwikowski, who explained the potential of new proteomic techniques for the determination of protein complexes, and showed several examples relevant to the study of transcription regulation.

The workshop included also a Poster session with 23 posters.

Assessment of the results & impact of the event

There are a number of indicators that allow us to be satisfied with the result for the meeting. Firstly, the number of participants was beyond our best estimation. Initially conceived for 50 participants we ended up with 64, and rejected more than 15 additional applications due to the limited capacity of the auditorium. Secondly, the number of posters: 23. These posters covered most of the topics of the workshop and given the quality of the work presented in them, we decided to select 6 of them to be included as short presentations, which again was extremely difficult due to extraordinary quality of the presented work.

Finally, as an additional sample of the impact of the workshop, we would like to mention also that "Genome Biology", one of the most important journal in the area featured a report for the meeting, written by 2 speakers and one of the participants [Teichmann, Bornberg-Bauer & Luscombe. "Transcriptional networking." Genome Biology 2005;6(9):344]

Programme
Thursday 26 May
9:00-11:00 Registration & Coffee
11:00-13:00 Modeling Networks (Chair: Alfonso Valencia)
Ricard Solé: Computation and tinkering in biological networks
Selected Poster: Jan T. Ki: transsys: A Framework for Modeling Gene Expression Dynamics Evaluating Network Reconstruction
Selected Poster: Adrian L. Garcia-Lomana: Studying the Dynamical Behavior of Gene Regulatory Networks with Byodyn
Hidde de Jong: Qualitative Modeling and Simulation of Genetic Regulatory Networks
13:00-14:30 Lunch
14:30-16:30 Posters Session
16:30-17:00 Coffee Break
17:00-19:00 Modeling Networks (cont) (Chair: Joaquin Dopazo)
Alvis Brazma: From microarray data to gene networks
Roderic Guigo: Finishing the Human Gene Set
Session Round up

Friday 27 May
9:00-10:30 Evolution of Transcription Networks (Chair: Erich Bornberg-Bauer)
Julio Collado-Vides: The Transcriptional and Regulatory Network of Escherichia coli K-12: Different Global Properties of the Network and their Biological Implications.
François Képès: On the Transcription-based Solenoidal Model of Chromosomes: Epigenomics of molecular networks
10:30-11:00 Coffee Break
11:00-13:00
Martijn Huynen: Predicting biomolecular systems and tracing their evolution
Selected Poster: David Ussery: Three Levels of Gene Regulation in Bacterial Genomes
Selected Poster: Rekin's Janky: A Taxonomy-Traversing Approach to Discover Cis-Acting Elements in Prokaryotes
Sarah A. Teichmann: Genome-wide transcription factor repertoire prediction and analysis
13:00-14:30 Lunch
14:30-16:30 Evolution of Transcription Networks II (Chair: Martijn Huynen)
Erich Bornberg-Bauer: Inferring the evolution of genetic regulation in eukaryotes from the analysis of a multitude of data.
Mar Albà: Variability and conservation in vertebrate promoters
Selected Poster: Nicholas M. Luscombe: Genomic Analysis of Regulatory Network Dynamics Reveals Large Topological Changes
Selected Poster: John M. Hancock: Simple Sequence Repeats in Proteins and their Significance for Network Evolution
16:30-17:00 Coffee Break
17:00-18:00 Frank C.P. Holstege: Unraveling transcriptional circuitry
Session Round up
20:00 Conference Dinner

Saturday 28 May
9:30-11:00 Connecting Transcription With Other Biological processes (Chair: Sarah Teichmann)
Jaques van Helden: Inferring meaningful pathways and functional distances in weighted metabolic networks
Benno Schwikowski: Computational support for the proteomic side of transcriptional networks
11:00-11:30 Coffee Break
11:30-12:30 Connecting Transcription With Other Biological processes (cont.)
Joaquin Dopazo: Relationship between connectivity and biological roles of genes in protein-protein interaction networks and transcriptional gene-interaction networks
Session Round Up
12:30-13:00 Closing Remarks